TReNA-class: Class TReNA

In TReNA: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Description

Class TReNA defines a TReNA object and contains an assay matrix, which contains expression data over a set of samples for a group of genes, and a string representing the name of a chosen solver.

Usage

TReNA(mtx.assay = matrix(), solver = "lasso", quiet = TRUE)

## S4 method for signature 'TReNA'
getSolverName(obj)

## S4 method for signature 'TReNA'
getSolverObject(obj)

Arguments

mtx.assay	An assay matrix of gene expression data
solver	A string matching the designated solver for relating a target gene to transcription factors. TReNA currently supports 9 solver strings (default = "lasso"): "lasso" "ridge" "randomForest" "bayesSpike" "sqrtlasso" "lassopv" "pearson" "spearman" "ensemble"
quiet	A logical denoting whether or not the TReNA object should print output
obj	An object of class TReNA

Value

An object of the TReNA class

Methods (by generic)

• getSolverName: Retrieve the name of the solver specified in a TReNA object

• getSolverObject: Retrieve the Solver object contained in a TReNA object

See Also

solve, Solver, getSolverName, getSolverObject

Examples

# Create a LassoSolver object using the included Alzheimer's data and retrieve the solver name
load(system.file(package="TReNA", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
solver <- TReNA(mtx.sub, solver = "lasso")
mtx <- getSolverName(solver)

# Create a LassoSolver object using the included Alzheimer's data and retrieve the solver object
load(system.file(package="TReNA", "extdata/ampAD.154genes.mef2cTFs.278samples.RData"))
solver <- TReNA(mtx.sub, solver = "lasso")
mtx <- getSolverObject(solver)

TReNA documentation built on Nov. 17, 2017, 12:35 p.m.